Here we present results from a long-term model simulation of the 3d coupled ecosystem model ECOSMO II for a North and Baltic Sea setup. The model allows both multi-decadal hindcast simulation of the marine system and specific process studies under controlled environmental conditions. Model results have been analysed with respect to long-term multi decadal variability in both physical and biological parameters with the help of empirical orthogonal function (EOF) analysis. The analysis of a 61-year (1948–2008) long hind cast reveals a quasi-decadal variation on salinity, temperature and current fields in the North Sea in addition to singular events of major changes during restricted time frames. These changes in hydrodynamic variables where found to be associated to changes in ecosystem productivity that are temporally aligned with the timing of reported <q>regime shifts</q> in the areas. Our results clearly indicate that for analysing ecosystem productivity spatially explicit methods are indispensable. Especially in the North Sea a correlation analysis between atmospheric forcing and primary production (PP) reveals significant correlations for NAO and wind forcing for the central part of the region, while AMO and air temperature are correlated to long-term changes in the southern North Sea frontal areas. Since correlations cannot serve to identify causal relationship we performed scenario model runs with perturbing the temporal variability in forcing condition emphasizing specifically the role of solar radiation, wind and eutrophication. The results revealed that, although all parameters are relevant for the magnitude of PP in the North Sea and Baltic Sea, the dominant impact on long-term variability and major shifts in ecosystem productivity was introduced by modulations of the wind fields.